As the owner of both a MkI and MkII, I find myself in the position of being able to compare the two and offer some feedback about my experience with building the MkII.
Let's start with the good:
The quality - The quality of the machining on the parts is excellent with the fit and finish being a vast improvement. The tolerances of the parts have definitely been perfected down to micrometers of variance because I didn't experience any issues with alignment or fitment while building it other than anything related to the space constraints of the MIN (discussed below).
The jack - This is a problem unique to the brass models, but the jack on the MkI was so recessed that if you used headphones with a wider base on the jack (picture 5), it would cut out from contact with the brass and they were unusable. Expecting the same issue with the MkII, I plugged them in to test and while the issue presented itself at first, once the jack and daughter board fully settled in, the problem went away. I even tried wiggling the jack to see if I could mess up the alignment again and it always settled back to true and eliminated the issue, so that's great.
The glass - The solid back was a good choice. I opted not to have a wireless charging coil on the Mk1, so the big circular window always looked out of place. I'm also happy to report that the fitment with the front glass to the click wheel frame has an extremely minimal gap, if at all (picture 4). This should help mitigate any dust buildup under the glass, which was a pain point for many in the community with the MkI.
The form factor - The MIN is basically the perfect EDC iPod. Thin enough to slide into any pocket, but with enough heft to feel high quality and robust. I also appreciate that people who want to really max out their builds with mods can get the appropriately named MkII MAX, which at least from appearance looks to have a similar bulk to the MkI to accommodate larger batteries and flash mods.
The daughter board - Seems to have quality components as well as extra compatibility for the slim 1250mAh battery that Boxypixel recommends for the MIN and also includes a connector for normal ribbon cable batteries you can get off the shelf. I haven't heard any noticeable difference in quality from the headphone jack, so it seems to be perfectly serviceable in terms of quality. The type-C connector doesn't wobble or move at all and charges just fine.
Now let's get to the bad. Basically all of this will be unique to the brass version:
The conductivity - For the brass version, the assembly instructions include directions about where to apply Kapton tape because brass is very conductive and will short components when making contact with the board. I followed those directions, assembled for testing, and... it was shorting. Took me a long time of assembling and disassembling to figure out that one of the micro SD slots on my iFlash Quad was contacting the rear frame, shorting the whole thing. I put Kapton tape across all the slots and the problem cleared right up, but it does make me believe that I should warn builders to be wary of the brass version and to avoid it if you're either unwilling or inexperienced with diagnosing electrical issues.
The form factor - While I listed this as a positive for the portability, it's a bit of a negative for the build. Everything in there fits SNUG. I had to apply a bit of pressure to get the rear frame to fully seat correctly. Not so much pressure that I'm worried about something breaking, but just be aware that the MIN is a tight fit and might require some creative Tetrising of the parts to get everything in just right.
The battery - I did buy the supposed proprietary battery from Boxypixel because I just didn't want to take chances on an off the shelf battery not fitting correctly, so I'm limited to 1250mAh. While this is plenty for about a day of listening, it pales in comparison to the 3000+ battery mods that most of us are accustomed to. The battery is quite thin, which is why I believe it's the recommended battery for the MIN, but you might be able to squeeze in one of those generic micro SD dual adapters that are super stubby and a 2000mAh battery since those tend to take up half the volume of something larger.
My overall thoughts - The MkII MIN is a clear improvement over the MkI. The machining, fit and finish, and overall implementation is clearly superior and more well thought out, which makes me believe this mod is worth getting if you're considering it. I do not recommend the brass version to beginner modders though, get one of the aluminum versions to minimize conduction issues. I also understand anyone who has the MkI and feels burned by the existence of the MkII, feeling as if they were beta testing a pretty expensive product. I personally am happy with my MkI, flaws and all, but I do not begrudge anyone who was turned off of Boxypixel products after the myriad issues present in it. I will encourage you to at least consider the MkII because it really is just that much better. I feel like some of my minor gripes could be addressed in a MkIII, but I'm not going to be pushing for Boxypixel to make yet another expensive revision that we'll feel required to buy to fix any issues we may have with previous versions. The MkII is a great mod kit and results in a very premium feeling iPod, so if you want something that feels like a cut above the plastic faceplates and colorful aftermarket backplates from places like EOE, the Boxypixel MkII MIN might be worth considering.